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Volumn 60, Issue 1, 2005, Pages 90-96

A consistent set of statistical potentials for quantifying local side-chain and backbone interactions

Author keywords

Boltzmann hypothesis; Fragment threading; Free energy; Knowledge based potentials; Side chain backbone interaction; Side chain side chain interaction

Indexed keywords

AMIDE; AMINO ACID; CARBONYL DERIVATIVE; PEPTIDE;

EID: 19544371352     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20482     Document Type: Article
Times cited : (35)

References (31)
  • 1
    • 0028053187 scopus 로고
    • Understanding how proteins fold: The lysozyme story so far
    • Dobson CM, Evans PA, Radford SE. Understanding how proteins fold: the lysozyme story so far. Trends Biochem Sci 1994;19:31-37.
    • (1994) Trends Biochem Sci , vol.19 , pp. 31-37
    • Dobson, C.M.1    Evans, P.A.2    Radford, S.E.3
  • 2
    • 0001842441 scopus 로고    scopus 로고
    • Adding backbone to protein folding: Why proteins are polypeptides
    • Honig B, Cohen FE. Adding backbone to protein folding: why proteins are polypeptides. Fold Des 1996;1:R17-R20.
    • (1996) Fold Des , vol.1
    • Honig, B.1    Cohen, F.E.2
  • 3
    • 0029961647 scopus 로고    scopus 로고
    • Structural analysis of non-native states of proteins by NMR methods
    • Shortle DR. Structural analysis of non-native states of proteins by NMR methods. Curr Opin Struct Biol 1996;6:24-30.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 24-30
    • Shortle, D.R.1
  • 4
    • 0035919635 scopus 로고    scopus 로고
    • Persistence of native-like topology in a denatured protein in 8 M urea
    • Shortle D, Ackerman MS. Persistence of native-like topology in a denatured protein in 8 M urea. Science 2001;293:487-489.
    • (2001) Science , vol.293 , pp. 487-489
    • Shortle, D.1    Ackerman, M.S.2
  • 5
    • 1842426942 scopus 로고    scopus 로고
    • Direct demonstration of structural similarity between native and denatured eglin C
    • Ohnishi S, Lee AL, Edgell MH, Shortle D. Direct demonstration of structural similarity between native and denatured eglin C. Biochemistry 2004;43:4064-4070.
    • (2004) Biochemistry , vol.43 , pp. 4064-4070
    • Ohnishi, S.1    Lee, A.L.2    Edgell, M.H.3    Shortle, D.4
  • 6
    • 0037137257 scopus 로고    scopus 로고
    • Robustness of the long-range structure in denatured staphylococcal nuclease to changes in amino acid sequence
    • Ackerman MS, Shortle D. Robustness of the long-range structure in denatured staphylococcal nuclease to changes in amino acid sequence. Biochemistry 2002;41:13791-13797.
    • (2002) Biochemistry , vol.41 , pp. 13791-13797
    • Ackerman, M.S.1    Shortle, D.2
  • 7
    • 0002006297 scopus 로고
    • Are there pathways for protein folding?
    • Levinthal C. Are there pathways for protein folding? J Chim Phys 1968;65:44-45.
    • (1968) J Chim Phys , vol.65 , pp. 44-45
    • Levinthal, C.1
  • 8
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 9
    • 0242267506 scopus 로고    scopus 로고
    • Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments
    • Fang Q, Shortle D. Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments. Proteins 2003;53(Suppl 6):486-490.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 486-490
    • Fang, Q.1    Shortle, D.2
  • 10
    • 0015244817 scopus 로고
    • Empirical protein energy maps
    • Pohl FM. Empirical protein energy maps. Nat New Biol 1971;234: 277-279.
    • (1971) Nat New Biol , vol.234 , pp. 277-279
    • Pohl, F.M.1
  • 11
    • 0017021957 scopus 로고
    • Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka S, Scheraga HA. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976;9:945-950.
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 12
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 13
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl MJ. Calculation of conformational ensembles from potentials of mean force: an approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 14
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
    • Kocher JP, Rooman MJ, Wodak SJ. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 1994;235:1598-1613.
    • (1994) J Mol Biol , vol.235 , pp. 1598-1613
    • Kocher, J.P.1    Rooman, M.J.2    Wodak, S.J.3
  • 15
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 1996;6:195-209.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 16
    • 0030914617 scopus 로고    scopus 로고
    • Comparison of database potentials and molecular mechanics force fields
    • Moult J. Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol 1997;7:194-199.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 194-199
    • Moult, J.1
  • 17
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 18
    • 0015967881 scopus 로고
    • Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins
    • Chou PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 1974;13:211-222.
    • (1974) Biochemistry , vol.13 , pp. 211-222
    • Chou, P.Y.1    Fasman, G.D.2
  • 19
    • 0037907478 scopus 로고    scopus 로고
    • Propensities, probabilities, and the Boltzmann hypothesis
    • Shortle D. Propensities, probabilities, and the Boltzmann hypothesis. Protein Sci 2003;12:1298-1302.
    • (2003) Protein Sci , vol.12 , pp. 1298-1302
    • Shortle, D.1
  • 20
    • 0036136694 scopus 로고    scopus 로고
    • Composites of local structure propensities: Evidence for local encoding of long-range structure
    • Shortle D. Composites of local structure propensities: evidence for local encoding of long-range structure. Protein Sci 2002;11:18-26.
    • (2002) Protein Sci , vol.11 , pp. 18-26
    • Shortle, D.1
  • 21
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82-95.
    • (1999) Proteins , vol.34 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 23
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein sequence through the folding motif
    • Bryant SH, Lawrence CE. An empirical energy function for threading protein sequence through the folding motif. Proteins 1993;16:92-112.
    • (1993) Proteins , vol.16 , pp. 92-112
    • Bryant, S.H.1    Lawrence, C.E.2
  • 24
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang G, Dunbrack RL, Jr. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 26
    • 0036219167 scopus 로고    scopus 로고
    • Improving the quality of protein structures derived by NMR spectroscopy
    • Spronk CA, Linge JP, Hilbers CW, Vuister GW. Improving the quality of protein structures derived by NMR spectroscopy. J Biomol NMR 2002;22:281-289.
    • (2002) J Biomol NMR , vol.22 , pp. 281-289
    • Spronk, C.A.1    Linge, J.P.2    Hilbers, C.W.3    Vuister, G.W.4
  • 27
    • 0034296491 scopus 로고    scopus 로고
    • Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force
    • Kuszewski J, Clore GM. Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force. J Magn Reson 2000;146:249-254.
    • (2000) J Magn Reson , vol.146 , pp. 249-254
    • Kuszewski, J.1    Clore, G.M.2
  • 28
    • 0346103679 scopus 로고    scopus 로고
    • Rapid protein fold determination using unassigned NMR data
    • Meiler J, Baker D. Rapid protein fold determination using unassigned NMR data. Proc Natl Acad Sci USA 2003;100:15404-15409.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 15404-15409
    • Meiler, J.1    Baker, D.2
  • 29
    • 0024836024 scopus 로고
    • A comparison of the CHARMM, AMBER and ECEPP potentials for peptides: II. Phi-psi maps for N-acetyl alanine N′-methyl amide: Comparisons, contrasts and simple experimental tests
    • Roterman IK, Lambert MH, Gibson KD, Scheraga HA. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides: II. Phi-psi maps for N-acetyl alanine N′-methyl amide: comparisons, contrasts and simple experimental tests. J Biomol Struct Dyn 1989;7:421-453.
    • (1989) J Biomol Struct Dyn , vol.7 , pp. 421-453
    • Roterman, I.K.1    Lambert, M.H.2    Gibson, K.D.3    Scheraga, H.A.4
  • 31
    • 0038008976 scopus 로고    scopus 로고
    • An improved protein decoy set for testing energy functions for protein structure prediction
    • Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 2003;53:76-87.
    • (2003) Proteins , vol.53 , pp. 76-87
    • Tsai, J.1    Bonneau, R.2    Morozov, A.V.3    Kuhlman, B.4    Rohl, C.A.5    Baker, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.